The accurate design of new protein-protein interactions is a longstanding goal of computational protein design. However, most computationally designed interfaces fail to form experimentally. This investigation compares five previously described successful de novo interface designs with 158 failures. Both sets of proteins were designed with the molecular modeling program Rosetta. Designs were considered a success if a high-resolution crystal structure of the complex closely matched the design model and the equilibrium dissociation constant for binding was less than 10 μM. The successes and failures represent a wide variety of interface types and design goals including heterodimers, homodimers, peptide-protein interactions, one-sided designs (i.e., where only one of the proteins was mutated) and two-sided designs. The most striking feature of the successful designs is that they have fewer polar atoms at their interfaces than many of the failed designs. Designs that attempted to create extensive sets of interface-spanning hydrogen bonds resulted in no detectable binding. In contrast, polar atoms make up more than 40% of the interface area of many natural dimers, and native interfaces often contain extensive hydrogen bonding networks. These results suggest that Rosetta may not be accurately balancing hydrogen bonding and electrostatic energies against desolvation penalties and that design processes may not include sufficient sampling to identify side chains in preordered conformations that can fully satisfy the hydrogen bonding potential of the interface.

译文

精确设计新的蛋白质-蛋白质相互作用是计算蛋白质设计的长期目标。但是,大多数计算设计的接口都无法通过实验形成。该调查比较了五个先前描述的成功的从头接口设计和158故障。两组蛋白质都是使用分子建模程序Rosetta设计的。如果配合物的高分辨率晶体结构与设计模型紧密匹配并且结合的平衡解离常数小于10μm,则认为设计是成功的。成功和失败代表了各种各样的界面类型和设计目标,包括异二聚体,同二聚体,肽-蛋白质相互作用,单面设计 (即仅其中一种蛋白质发生突变) 和双面设计。成功设计的最显着特征是,与许多失败的设计相比,它们在界面上的极性原子更少。试图创建广泛的跨界面氢键集的设计导致无法检测到结合。相反,极性原子占许多天然二聚体的界面面积的40% 以上,并且天然界面通常包含广泛的氢键网络。这些结果表明,Rosetta可能无法准确地平衡氢键和静电能免受去溶剂化的影响,并且设计过程可能不包括足够的采样来识别可以完全满足界面氢键电势的预定构象中的侧链。

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